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Platform documentation

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Tips and tricks

GET STARTED

About the Seven Bridges Platform
- Time synchronization
Before you start
QuickStart
Account settings
About the Payments page
Manage your subscription
Cloud infrastructure pricing
Developer Dashboard
Email notifications page

TUTORIALS

Seven Bridges Platform tutorials
Build a workflow tutorial
Worked example of uploading SAMtools Sort
Upload a custom Python program using a Dockerfile
Create a tar archive
Troubleshooting tutorial
Comprehensive tips for reliable and efficient analysis set-up

ACCESS THE SEVEN BRIDGES PLATFORM

Sign up for the Seven Bridges Platform
Access via the visual interface
Access via the API
Set up two-factor authentication

MANAGE AN ANALYSIS ENVIRONMENT

Projects on the Seven Bridges Platform
Create a project
View a project
Manage the project dashboard
Modify project settings
Set file download restriction
Manage email notifications
Add notes to your project
Leave a project
Delete a project
Tag your projects

COLLABORATE SECURELY

Collaboration on the Seven Bridges Platform
Add a collaborator to a project
Set permissions

DATASETS HUB

About datasets

BRING YOUR PRIVATE DATA

Upload your data to the Seven Bridges Platform
Upload from your computer
Upload via the command line
Import from an FTP/HTTP(S) server
Upload via the API
Import from a Volume
Import from a DRS server

SET METADATA ASSOCIATED WITH A FILE

Metadata on the Seven Bridges Platform
- System metadata
- Metadata schema
Edit metadata using the visual interface
- Edit metadata with a manifest
- Export metadata to a manifest
Edit metadata using the command line uploader
Edit metadata using the API
Metadata manifest file format

SEARCH FILES

File repositories on the Seven Bridges Platform
Search files on the Platform

ADD FILES TO A PROJECT

Add files using the visual interface
Copy files using the API
Tag your files

ORGANIZE FILES

Available actions
Activity center
New File Browser

ARCHIVE FILES (on AWS)

File archiving overview
Archive a file
Restore a file
Delete an archived file

ARCHIVE APPS

App archiving overview
Archive an app
Restore an app

SBFS (Beta)

About SBFS
Install SBFS automatically
Install SBFS manually
Configure SBFS credentials
List available projects for SBFS
Mount a project
Unmount a project
Command reference
SBFS Log
Upgrade SBFS
Uninstall SBFS

FIND APPS

Apps on the Seven Bridges Platform
- Publish a third-party app or workflow
Search for an app
Explore app details
App versions
Interactive Web Apps

BRING YOUR TOOLS

About the SDK
About the Common Workflow Language
CWL v.1.0 improvements over sbg:draft-2
CWL v1.2 conditional execution
Bring Nextflow apps to the Platform
Bring WDL apps to the Platform

DOCKER

About Docker
Install Docker
Image registries
- About the Seven Bridges Image Registry
- About Docker Hub
Create and upload a Docker image
Create and upload a Docker image with a Dockerfile
Manage Docker repositories
Core Docker commands
Docker for Enterprise
Mount a USB drive in a Docker container
Docker best practice recommendations

DESCRIBE YOUR TOOL (LEGACY)

The Tool Editor
General tool information
Tool input ports
Tool output ports
Additional tool information
Test the tool description
Dynamic Expressions in Tool Descriptions
Advanced features of the tool editor
Forking tools

TOOL WRAPPING TIPS AND TRICKS

Tips and tricks

COPY AN APP

Copy public apps to a project
Copy an app from a project

EDIT AN APP (LEGACY)

Edit a tool
Create a workflow
Edit a workflow
Add revision notes

Edit an app

About the editor
The tool editor
The workflow editor

RUN AN ANALYSIS

About analyses
About batch analyses
Run a task
Define app settings
Set computation instances
About secondary (index) files

TASK EXECUTION

About task execution
About controlling task execution
About parallelizing tool executions (Scatter)
About tool resource requirements
About Memoization (Reuse)
Project and file locations (Multi-cloud)
Set execution hints at workflow level
Set execution hints at node level
Set execution hints at tool level
Set execution hints at task level
About Spot Instances
Use Spot Instances
List of execution hints
List of task statuses
List of available Amazon Web Services US instances
List of available Amazon Web Services EU instances

REVIEW A TASK

Review the task page
View task stats
View task logs
Job retry
View instance metrics
Real-time job monitoring
Troubleshoot a failed task

VIEW ANALYSIS RESULTS

View output files

INTERACTIVE ANALYSIS

Interactive analysis on the Platform
Seven Bridges Genome Browser
Variant Browser
VCF Benchmarking app
CummeRbundQC RNA-Seq Visualization
FastQC
Picard Collect Alignment Summary Metrics
The Seven Bridges Coverage app

RHEO

Overview
Manage via CLI
Manage via API
Manage via RHEO visual interface (GUI)
RHEO glossary

RHEO FOR DEVELOPERS

Overview
RHEO Developer tutorial
Create automations for the RHEO visual interface (GUI)
- Automation inputs
- Automation outputs

GRAPH GENOME APPS

About Graph Genome apps
Graph WGS
- About Graph WGS
- Graph Germline Variant Detection Workflow tutorial

DATA STUDIO

About Data Studio
JupyterLab quick reference
RStudio quick reference
Run a Data Studio analysis
Data Studio analysis details
Copy a Data Studio analysis
Data Studio analysis charging
Data Studio analysis editor
Data Studio environments and libraries
Data Studio Session Activity and Automatic Logout

DOWNLOAD RESULTS

Download results

DEVELOPER TOOLS

Developer Hub
Get your authentication token
Publish your app in the Public Apps gallery
Integrate your web application

PUBLIC PROJECTS

Public projects overview
Smart Variant Filtering
Data Studio Interactive Analyses
VCF Benchmarking
Cancer Cell Line Encyclopedia (CCLE)
Simons Genome Diversity Project (SGDP) dataset
Human Cell Atlas Preview Datasets

ENTERPRISE FEATURES

About the Enterprise feature
Collaboration within an Enterprise
Manage an Enterprise
Manage a Division
Add a collaborator to an Enterprise project
Switch between Divisions
Manage two-factor authentication
Manage Docker repositories
Single sign-on (SSO) setup

API Hub

API Overview
API tutorials
API rate limit
Using volumes via the API

API CLIENTS

API Clients
Store credentials to access Seven Bridges client applications and libraries
R library
Python library recipes
Python library
Java library
Java library Quickstart
Seven Bridges Command Line Interface
Seven Bridges Command Line Interface Reference

Connect cloud storage

Connect cloud storage overview
Volumes
Aliases
Supported cloud storage providers
Amazon Web Services Simple Storage Service (AWS S3) Volumes
Google Cloud Storage (GCS) Volumes
Security concerns when working with volumes
Enabling cross-origin resource sharing (CORS)
Operations on volumes
API Cloud storage tutorials
- AWS Cloud storage tutorial
- Google Cloud Storage tutorial

GLOSSARY

Glossary

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Tips and tricks

Contents

Make files available in your tool's working directory
Set the default value for an input port
JavaScript Cookbook

Updated 10 months ago

Make files available in your tool's working directory

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